info_by_county <- CensusHLA::census_adjusted_nmdp_hla_frequencies_by_county |>
dplyr::filter(!(state %in% c('Alaska','Hawaii'))) |>
dplyr::filter(allele == 'B*58:01')
out_data <- info_by_county |>
dplyr::ungroup() |>
dplyr::filter(allele == 'B*58:01') |>
dplyr::group_by(region, state, census_region, county, fips, loci, allele) |>
dplyr::summarize(gf = sum(us_2020_nmdp_gf)) |>
dplyr::filter(!(is.na(gf))) |>
# Create a STATEFP and COUNTYFP column by breaking the fips column on the 3rd character to the end
dplyr::mutate(STATEFP = substr(fips, 1, 2),
COUNTYFP = substr(fips, 3, nchar(fips)))
out_data <-
out_data |>
dplyr::mutate(
county = dplyr::case_when(
state == "Connecticut" &
census_region == "Litchfield County, Connecticut" ~ "Northwest Hills Planning Region",
state == "Connecticut" &
census_region == "Hartford County, Connecticut" ~ "Capitol Planning Region",
state == "Connecticut" &
census_region == "Middlesex County, Connecticut" ~ "Lower Connecticut River Valley Planning Region",
state == "Connecticut" &
census_region == "Windham County, Connecticut" ~ "Northeastern Connecticut Planning Region",
state == "Connecticut" &
census_region == "New Haven County, Connecticut" ~ "South Central Connecticut Planning Region",
state == "Connecticut" &
census_region == "New London Count, Connecticut" ~ "Southeastern Connecticut Planning Region",
state == "Connecticut" &
census_region == "Fairfield County, Connecticut" ~ "Western Connecticut Planning Region",
state == "Connecticut" &
census_region == "Tolland County" ~ "Capitol Planning Region",
census_region == "Doña Ana County" ~ "Donna Ana County",
census_region == "Chugach Census Area" ~ "Valdez-Cordova Census Area",
census_region == "Copper River Census Area" ~ "Valdez-Cordova Census Area",
T ~ census_region
)) |>
dplyr::mutate(
fips = dplyr::case_when(state == "Connecticut" & county == "Northwest Hills Planning Region" ~ "09160",
state == "Connecticut" & county == "Greater Bridgeport Planning Region" ~ "09120",
state == "Connecticut" & county == "Lower Connecticut River Valley Planning Region" ~ "09130",
state == "Connecticut" & county == "Naugatuck Valley Planning Region" ~ "09140",
state == "Connecticut" & county == "Northeastern Connecticut Planning Region" ~ "09150",
state == "Connecticut" & county == "South Central Connecticut Planning Region" ~ "09170",
state == "Connecticut" & county == "Southeastern Connecticut Planning Region" ~ "09180",
state == "Connecticut" & county == "Western Connecticut Planning Region" ~ "09190",
state == "Connecticut" & county == "Capitol Planning Region" ~ "09110",
T ~ fips)
)
gg_b58_by_county <-
usmap::plot_usmap(
data = out_data,
regions = "counties",
exclude = c('AK','HI'),
#include = c('AK', 'HI'),
values = "gf",
color = "black",
linewidth = 0.1
) +
viridis::scale_fill_viridis(option = "plasma", direction = 1)
gg_b58_by_county